* Package: sci-biology/vienna-rna-2.1.8 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python python_targets_python2_7 userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking ViennaRNA-2.1.8.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... * Applying vienna-rna-2.1.8-bindir.patch ... [ ok ] * Applying vienna-rna-2.1.1-prll.patch ... [ ok ] * Applying vienna-rna-2.1.1-impl-decl.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' ... * Running aclocal ... [ ok ] * This package has a configure.in file which has long been deprecated. Please * update it to use configure.ac instead as newer versions of autotools will die * when it finds this file. See https://bugs.gentoo.org/426262 for details. * Running autoconf --force ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: ViennaRNA-2.1.8/ * Running elibtoolize in: ViennaRNA-2.1.8/Kinfold/ * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/ * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/g2-0.70/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" * econf: updating ViennaRNA-2.1.8/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/vienna-rna-2.1.8 --enable-shared --disable-static --with-cluster --disable-openmp --without-doc-pdf --without-doc-html --without-doc checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking whether make sets $(MAKE)... (cached) yes checking for grep that handles long lines and -e... /bin/grep checking for exp in -lm... yes checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for strrchr... yes checking for strstr... (cached) yes checking for strtol... yes checking for strtoul... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for erand48... yes checking for memset... yes checking for memmove... yes checking for erand48... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for interfaces/Perl/Makefile.am... yes checking for Kinfold/Makefile.am... yes checking for RNAforester/Makefile.am... yes checking for Cluster/Makefile.am... yes checking for libsvm-2.91/svm.cpp... yes checking for libsvm-2.91/svm.h... yes checking whether float precision is used for partition function arrays instead of double precision... no checking for perl... /usr/bin/perl checking for python... /usr/bin/python configure: WARNING: You need Python >= 2.5 and < 3.0 to build the Python extension configure: WARNING: You may set the PythonCmd environment variable to point to a suitable python binary checking for doxygen... /usr/bin/doxygen checking for pdflatex... /usr/bin/pdflatex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for dot... /usr/bin/dot checking for egrep... /bin/egrep checking for perl... /usr/bin/perl checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating interfaces/Perl/Makefile config.status: creating interfaces/Perl/Makefile.PL config.status: creating Cluster/Makefile config.status: creating misc/Makefile config.status: creating misc/ViennaRNA.spec config.status: creating misc/PKGBUILD config.status: creating interfaces/Makefile config.status: creating Makefile config.status: creating RNAlib2.pc config.status: creating Utils/Makefile config.status: creating Progs/Makefile config.status: creating lib/Makefile config.status: creating man/Makefile config.status: creating H/Makefile config.status: creating doc/Makefile config.status: creating man/cmdlopt.sh config.status: creating config.h config.status: executing depfiles commands === configuring in Kinfold (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for strdup... yes checking for memset... yes checking for strchr... yes checking for ViennaRNA package... headers in "../H" and library... "../lib" checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking fold.h usability... yes checking fold.h presence... yes checking for fold.h... yes checking for exp in -lm... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none using (to be built) libRNA.a in ../lib checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.70 (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/install -c checking for find... find checking for makedepend... makedepend checking for dlopen in -ldl... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lgd... yes checking for gdImagePng... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL Supported devices: PostScript FIG X11 Unsupported devices: Win32 GD Run 'make depend' to create dependencies. configure: Configure successful with the following options: RNAlib Interfaces: Perl Interface: yes Python Interface: no Ruby Interface: no Extra Programs: Analyse{Dists,Seqs}: yes Kinfold: yes RNAforester: yes Other Options: SVM: yes Documentation: no (HTML): no (PDF): no - Files will be installed in the following directories: Executables: /usr/bin Libraries: /usr/lib64 Header files: /usr/include Extra Data: /usr/share Man pages: /usr/share/man Documentation: /usr/share/doc/vienna-rna-2.1.8 (HTML): /usr/share/doc/vienna-rna-2.1.8/html (PDF): /usr/share/doc/vienna-rna-2.1.8 >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' Making all in lib make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c treedist.c: In function ‘print_postorder_list’: treedist.c:437:13: warning: type defaults to ‘int’ in declaration of ‘i’ [-Wimplicit-int] register i; ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c naview.c: In function ‘dump_loops’: naview.c:341:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] printf("\nRoot loop is #%d\n",(root-loops)+1); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c LPfold.c: In function ‘putoutpU_splitup’: LPfold.c:1012:14: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=] fprintf(fp,"\t%s\n",ident); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-convert_epars.o `test -f 'convert_epars.c' || echo './'`convert_epars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c MEA.c: In function ‘mea_backtrack’: MEA.c:223:9: warning: implicit declaration of function ‘get_gquad_pattern_pf’ [-Wimplicit-function-declaration] get_gquad_pattern_pf(S, i, j, pf, &L, l); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-aliLfold.o `test -f 'aliLfold.c' || echo './'`aliLfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-mm.o `test -f 'mm.c' || echo './'`mm.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dfold.o `test -f '2Dfold.c' || echo './'`2Dfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dpfold.o `test -f '2Dpfold.c' || echo './'`2Dpfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plex_functions.o `test -f 'plex_functions.c' || echo './'`plex_functions.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plot_layouts.o `test -f 'plot_layouts.c' || echo './'`plot_layouts.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c ali_plex.c: In function ‘alifind_max’: ali_plex.c:595:27: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, ^ ali_plex.c: In function ‘aliplot_max’: ali_plex.c:643:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c c_plex.c: In function ‘find_max_C’: c_plex.c:1071:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, ^ c_plex.c: In function ‘plot_max_C’: c_plex.c:1112:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c plex.c: In function ‘find_max_XS’: plex.c:1511:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf(" %s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2 ^ plex.c: In function ‘plot_max_XS’: plex.c:1607:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5. ^ plex.c: In function ‘find_max’: plex.c:2671:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, ^ plex.c:2718:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, ^ plex.c: In function ‘plot_max’: plex.c:2753:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, ^ plex.c:2775:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-snofold.o `test -f 'snofold.c' || echo './'`snofold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.c snoop.c: In function ‘find_max_snoop’: snoop.c:1087:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f ^ snoop.c: In function ‘snoop_subopt_XS’: snoop.c:1600:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f ^ snoop.c: In function ‘find_max_snoop_XS’: snoop.c:2096:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-move_set.o `test -f 'move_set.c' || echo './'`move_set.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-gquad.o `test -f 'gquad.c' || echo './'`gquad.c x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -march=native -O2 -pipe -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp ../libsvm-2.91/svm.cpp: In function ‘svm_model* svm_load_model(const char*)’: ../libsvm-2.91/svm.cpp:2730:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%80s",cmd); ^ ../libsvm-2.91/svm.cpp:2734:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%80s",cmd); ^ ../libsvm-2.91/svm.cpp:2756:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%80s",cmd); ^ ../libsvm-2.91/svm.cpp:2777:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",¶m.degree); ^ ../libsvm-2.91/svm.cpp:2779:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%lf",¶m.gamma); ^ ../libsvm-2.91/svm.cpp:2781:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%lf",¶m.coef0); ^ ../libsvm-2.91/svm.cpp:2783:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&model->nr_class); ^ ../libsvm-2.91/svm.cpp:2785:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&model->l); ^ ../libsvm-2.91/svm.cpp:2791:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%lf",&model->rho[i]); ^ ../libsvm-2.91/svm.cpp:2798:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&model->label[i]); ^ ../libsvm-2.91/svm.cpp:2805:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%lf",&model->probA[i]); ^ ../libsvm-2.91/svm.cpp:2812:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%lf",&model->probB[i]); ^ ../libsvm-2.91/svm.cpp:2819:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&model->nSV[i]); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-svm_utils.o `test -f 'svm_utils.c' || echo './'`svm_utils.c rm -f libRNA.a ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-convert_epars.o libRNA_a-MEA.o libRNA_a-aliLfold.o libRNA_a-mm.o libRNA_a-2Dfold.o libRNA_a-2Dpfold.o libRNA_a-plex_functions.o libRNA_a-plot_layouts.o libRNA_a-ali_plex.o libRNA_a-c_plex.o libRNA_a-plex.o libRNA_a-snofold.o libRNA_a-snoop.o libRNA_a-move_set.o libRNA_a-gquad.o svm.o libRNA_a-svm_utils.o x86_64-pc-linux-gnu-ranlib libRNA.a make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' Making all in Progs make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAfold_cmdl.o RNAfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAfold.o RNAfold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold_cmdl.o RNAfold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAeval_cmdl.o RNAeval_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAeval.o RNAeval.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval_cmdl.o RNAeval.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAheat_cmdl.o RNAheat_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAheat.o RNAheat.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat_cmdl.o RNAheat.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApdist_cmdl.o RNApdist_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApdist.o RNApdist.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist_cmdl.o RNApdist.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAdistance_cmdl.o RNAdistance_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAdistance.o RNAdistance.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAinverse_cmdl.o RNAinverse_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAinverse.o RNAinverse.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplot_cmdl.o RNAplot_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplot.o RNAplot.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot_cmdl.o RNAplot.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsubopt_cmdl.o RNAsubopt_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsubopt.o RNAsubopt.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALfold_cmdl.o RNALfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALfold.o RNALfold.c x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold_cmdl.o RNALfold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAcofold_cmdl.o RNAcofold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAcofold.o RNAcofold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApaln_cmdl.o RNApaln_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApaln.o RNApaln.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln_cmdl.o RNApaln.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAduplex_cmdl.o RNAduplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAduplex.o RNAduplex.c RNAduplex.c: In function ‘main’: RNAduplex.c:161:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat=] if (istty) printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); ^ RNAduplex.c:161:23: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] RNAduplex.c: In function ‘print_struc’: RNAduplex.c:202:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex_cmdl.o RNAduplex.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAalifold_cmdl.o RNAalifold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAalifold.o RNAalifold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplfold.o RNAplfold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAup_cmdl.o RNAup_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAup.o RNAup.c RNAup.c: In function ‘main’: RNAup.c:346:5: warning: implicit declaration of function ‘read_parameter_file’ [-Wimplicit-function-declaration] read_parameter_file(ParamFile); ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAup RNAup_cmdl.o RNAup.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAaliduplex.o RNAaliduplex.c RNAaliduplex.c: In function ‘print_struc’: RNAaliduplex.c:170:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALalifold.o RNALalifold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNA2Dfold.o RNA2Dfold.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAparconv.o RNAparconv.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAPKplex.o RNAPKplex.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplex_cmdl.o RNAplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplex.o RNAplex.c RNAplex.c: In function ‘main’: RNAplex.c:1100:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t {aka long unsigned int}’ [-Wformat=] printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); ^ RNAplex.c:1100:16: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplex RNAplex_cmdl.o RNAplex.o ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsnoop.o RNAsnoop.c RNAsnoop.c: In function ‘print_struc’: RNAsnoop.c:542:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4 ^ RNAsnoop.c: In function ‘aliprint_struc’: RNAsnoop.c:623:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat=] printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4 ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../lib/libRNA.a -lm -lm make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' Making all in man make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' Making all in Utils make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o b2ct.o b2ct.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o popt.o popt.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o ct2db_cmdl.o ct2db_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o ct2db.o ct2db.c ct2db.c: In function ‘main’: ct2db.c:156:13: warning: implicit declaration of function ‘MEA_seq’ [-Wimplicit-function-declaration] mea = MEA_seq(pairs, seq, structure, MEAgamma, params); ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ct2db ct2db_cmdl.o ct2db.o -L../lib -lRNA -lm -lm if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' switch.pl ; \ fi make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' Making all in H make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' Making all in misc make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' Making all in doc make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' Making all in interfaces make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' Making all in Perl make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' /usr/bin/perl Makefile.PL INSTALLDIRS=vendor PREFIX=/usr INSTALL_BASE= Generating a Unix-style Makefile.perl Writing Makefile.perl for RNA Writing MYMETA.yml and MYMETA.json make -f Makefile.perl make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' cp RNA.pm blib/lib/RNA.pm Running Mkbootstrap for RNA () chmod 644 "RNA.bs" x86_64-pc-linux-gnu-gcc -c -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=native -O2 -pipe -I../../H -O2 -pipe -DVERSION=\"2.1.8\" -DXS_VERSION=\"2.1.8\" -fPIC "-I/usr/lib64/perl5/5.24.0/x86_64-linux/CORE" RNA_wrap.c RNA_wrap.c: In function ‘my_alifold’: RNA_wrap.c:2316:23: warning: passing argument 1 of ‘alifold’ from incompatible pointer type [-Wincompatible-pointer-types] *energy = alifold(strings, struc); ^ In file included from RNA_wrap.c:1578:0: ../../H/../H/alifold.h:86:8: note: expected ‘const char **’ but argument is of type ‘char **’ float alifold( const char **strings, ^ RNA_wrap.c: In function ‘_wrap_LoopEnergy’: RNA_wrap.c:6632:5: warning: ‘LoopEnergy’ is deprecated [-Wdeprecated-declarations] result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:523:16: note: declared here DEPRECATED(int LoopEnergy(int n1, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_HairpinE’: RNA_wrap.c:6707:5: warning: ‘HairpinE’ is deprecated [-Wdeprecated-declarations] result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:536:16: note: declared here DEPRECATED(int HairpinE(int size, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_initialize_fold’: RNA_wrap.c:6742:5: warning: ‘initialize_fold’ is deprecated [-Wdeprecated-declarations] initialize_fold(arg1); ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:547:17: note: declared here DEPRECATED(void initialize_fold(int length)); ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_struct’: RNA_wrap.c:6780:5: warning: ‘energy_of_struct’ is deprecated [-Wdeprecated-declarations] result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:563:18: note: declared here DEPRECATED(float energy_of_struct(const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_struct_pt’: RNA_wrap.c:6835:5: warning: ‘energy_of_struct_pt’ is deprecated [-Wdeprecated-declarations] result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:582:16: note: declared here DEPRECATED(int energy_of_struct_pt( const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_circ_struct’: RNA_wrap.c:6879:5: warning: ‘energy_of_circ_struct’ is deprecated [-Wdeprecated-declarations] result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2 ^ In file included from RNA_wrap.c:1560:0: ../../H/../H/fold.h:601:18: note: declared here DEPRECATED(float energy_of_circ_struct( const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_initialize_cofold’: RNA_wrap.c:7403:5: warning: ‘initialize_cofold’ is deprecated [-Wdeprecated-declarations] initialize_cofold(arg1); ^ In file included from RNA_wrap.c:1561:0: ../../H/../H/cofold.h:180:17: note: declared here DEPRECATED(void initialize_cofold(int length)); ^ ../../H/../H/cofold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_init_pf_fold’: RNA_wrap.c:8311:5: warning: ‘init_pf_fold’ is deprecated [-Wdeprecated-declarations] init_pf_fold(arg1); ^ In file included from RNA_wrap.c:1562:0: ../../H/../H/part_func.h:407:17: note: declared here DEPRECATED(void init_pf_fold(int length)); ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_centroid’: RNA_wrap.c:8347:5: warning: ‘centroid’ is deprecated [-Wdeprecated-declarations] result = (char *)centroid(arg1,arg2); ^ In file included from RNA_wrap.c:1562:0: ../../H/../H/part_func.h:413:18: note: declared here DEPRECATED(char *centroid(int length, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_mean_bp_dist’: RNA_wrap.c:8377:5: warning: ‘mean_bp_dist’ is deprecated [-Wdeprecated-declarations] result = (double)mean_bp_dist(arg1); ^ In file included from RNA_wrap.c:1562:0: ../../H/../H/part_func.h:421:19: note: declared here DEPRECATED(double mean_bp_dist(int length)); ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_expLoopEnergy’: RNA_wrap.c:8461:5: warning: ‘expLoopEnergy’ is deprecated [-Wdeprecated-declarations] result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ In file included from RNA_wrap.c:1562:0: ../../H/../H/part_func.h:426:19: note: declared here DEPRECATED(double expLoopEnergy(int u1, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_expHairpinEnergy’: RNA_wrap.c:8536:5: warning: ‘expHairpinEnergy’ is deprecated [-Wdeprecated-declarations] result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); ^ In file included from RNA_wrap.c:1562:0: ../../H/../H/part_func.h:438:19: note: declared here DEPRECATED(double expHairpinEnergy( int u, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_Make_bp_profile’: RNA_wrap.c:11742:5: warning: ‘Make_bp_profile’ is deprecated [-Wdeprecated-declarations] result = (float *)Make_bp_profile(arg1); ^ In file included from RNA_wrap.c:1571:0: ../../H/../H/profiledist.h:56:19: note: declared here DEPRECATED(float *Make_bp_profile(int length)); ^ ../../H/../H/profiledist.h:5:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_copy_parameters’: RNA_wrap.c:13291:5: warning: ‘copy_parameters’ is deprecated [-Wdeprecated-declarations] result = (paramT *)copy_parameters(); ^ In file included from RNA_wrap.c:1576:0: ../../H/../H/params.h:126:24: note: declared here DEPRECATED(paramT *copy_parameters(void)); ^ ../../H/../H/params.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_set_parameters’: RNA_wrap.c:13317:5: warning: ‘set_parameters’ is deprecated [-Wdeprecated-declarations] result = (paramT *)set_parameters(arg1); ^ In file included from RNA_wrap.c:1576:0: ../../H/../H/params.h:127:24: note: declared here DEPRECATED(paramT *set_parameters(paramT *dest)); ^ ../../H/../H/params.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_PS_dot_plot’: RNA_wrap.c:14984:5: warning: ‘PS_dot_plot’ is deprecated [-Wdeprecated-declarations] result = (int)PS_dot_plot(arg1,arg2); ^ In file included from RNA_wrap.c:1566:0: ../../H/../H/PS_dot.h:195:16: note: declared here DEPRECATED(int PS_dot_plot( char *string, ^ ../../H/../H/PS_dot.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ rm -f blib/arch/auto/RNA/RNA.so g++ -shared -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed RNA_wrap.o -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/RNA/RNA.so ../../lib/libRNA.a \ -lm \ chmod 755 blib/arch/auto/RNA/RNA.so "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- RNA.bs blib/arch/auto/RNA/RNA.bs 644 Manifying 1 pod document make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' Making all in Cluster make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o split.o split.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o distance_matrix.o distance_matrix.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o cluster.o cluster.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o treeplot.o treeplot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o AD_main.o AD_main.c AD_main.c:16:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main(int argc, char *argv[]) ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c ./../lib/utils.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o statgeom.o statgeom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o AS_main.o AS_main.c AS_main.c:21:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main(int argc, char *argv[]) ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o PS3D.o PS3D.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o utils.o -lm -lm make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster' Making all in Kinfold make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/missing autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' Making all in Example make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example' make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o baum.o baum.c baum.c: In function ‘ini_or_reset_rl’: baum.c:206:7: warning: implicit declaration of function ‘initialize_cofold’ [-Wimplicit-function-declaration] initialize_cofold(GSV.len); ^ baum.c:208:19: warning: implicit declaration of function ‘cofold’ [-Wimplicit-function-declaration] GAV.sE[0] = cofold(GAV.farbe_full, GAV.stopform[0]); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o cache.o cache.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o globals.o globals.c globals.c: In function ‘process_options_gg’: globals.c:298:25: warning: passing argument 2 of ‘strncpy’ makes pointer from integer without a cast [-Wint-conversion] strncpy(GAV.ParamFile,255,args_info.Par_arg); ^ In file included from /usr/include/features.h:368:0, from /usr/include/stdio.h:27, from globals.c:9: /usr/include/bits/string3.h:123:1: note: expected ‘const char * restrict’ but argument is of type ‘int’ __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ globals.c:298:29: warning: passing argument 3 of ‘strncpy’ makes integer from pointer without a cast [-Wint-conversion] strncpy(GAV.ParamFile,255,args_info.Par_arg); ^ In file included from /usr/include/features.h:368:0, from /usr/include/stdio.h:27, from globals.c:9: /usr/include/bits/string3.h:123:1: note: expected ‘size_t {aka long unsigned int}’ but argument is of type ‘char *’ __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ globals.c:331:39: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat=] if (sscanf(args_info.pbounds_arg, "%g=%g=%g", ^ globals.c:331:39: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat=] globals.c:331:39: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat=] globals.c: In function ‘process_options’: globals.c:420:23: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat=] if (sscanf(optarg, "%g=%g=%g", ^ globals.c:420:23: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat=] globals.c:420:23: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat=] x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o main.o main.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o nachbar.o nachbar.c nachbar.c: In function ‘sel_nb’: nachbar.c:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=] sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o cmdline.o cmdline.c x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' Making all in RNAforester make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/missing autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/sh ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' Making all in g2-0.70 make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o src/FIG/g2_FIG.c: In function ‘g2_FIG_draw_string’: src/FIG/g2_FIG.c:477:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t {aka long unsigned int}’ [-Wformat=] fprintf(fig->fp,"4 0 %d 1 -1 0 %d 0 5 %d %d %d %d ", ^ x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o ar -cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o test ! -n "x86_64-pc-linux-gnu-ranlib" || x86_64-pc-linux-gnu-ranlib libg2.a test -d ./include || mkdir ./include cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/ make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' Making all in src make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o Arguments.o Arguments.cpp x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o glib.o glib.c glib.c: In function ‘ReadGraph’: glib.c:161:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d %c",size,&edges,&c); ^ glib.c:170:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d%d%d",°ree,&vlabel,&xcoord,&ycoord); ^ glib.c:176:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d", &adj_node, &elabel); ^ glib.c: In function ‘ReadEuclid’: glib.c:225:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d %c",size,&c); ^ glib.c:234:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d",&xcoord,&ycoord); ^ glib.c: In function ‘ReadMatrix’: glib.c:272:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d %c",size,&c); ^ glib.c:282:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&k); ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o main.o main.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o ppforestbase.o ppforestbase.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o progressive_align.o progressive_align.cpp progressive_align.cpp: In function ‘node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix*, double)’: progressive_align.cpp:341:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] WriteGraph (graph,"test.out"); ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_profile_alignment.o rna_profile_alignment.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_alignment.o rna_alignment.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_algebra.o rna_algebra.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_alphabet.o rna_alphabet.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforest.o rnaforest.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforestsz.o rnaforestsz.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnafuncs.o rnafuncs.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforester_options.o rnaforester_options.cpp x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o wmatch.o wmatch.c x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -L../g2-0.70 -L../../lib -L../../ViennaRNA -Wl,-O1 -Wl,--as-needed -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o -lg2 -lRNA make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src' Making all in man make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man' make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' make[1]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j1 -C Readseq build CC=x86_64-pc-linux-gnu-gcc make: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' Compiling readseq... x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe -o readseq readseq.c ureadseq.c ureadasn.c readseq.c: In function ‘formatstr’: readseq.c:257:34: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] case kASNseqset : return formats[kASN1-1]; ^ readseq.c:259:38: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] case kPhylipSequential: return formats[kPhylip-1]; ^ readseq.c:263:15: warning: return discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] else return formats[format-1]; ^ readseq.c: In function ‘usage’: readseq.c:328:3: warning: format not a string literal and no format arguments [-Wformat-security] fprintf(stderr,title); ^ readseq.c: In function ‘chooseFormat’: readseq.c:419:7: warning: implicit declaration of function ‘gets’ [-Wimplicit-function-declaration] gets(sform); ^ readseq.c: At top level: readseq.c:712:1: warning: return type defaults to ‘int’ [-Wimplicit-int] main( int argc, char *argv[]) ^ readseq.c: In function ‘main’: readseq.c:768:3: warning: format not a string literal and no format arguments [-Wformat-security] if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title); ^ readseq.c:910:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] sprintf( stemp,"%s_%d", oname, whichSeq); ^ readseq.c:912:29: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp ^ readseq.c:954:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, ^ readseq.c:954:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] readseq.c:954:28: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] readseq.c:965:15: warning: format not a string literal and no format arguments [-Wformat-security] if (seqout == 0) fprintf( foo, kASN1headline); ^ readseq.c:972:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ^ readseq.c:972:50: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] readseq.c:973:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] else fprintf(foo," %d %d YF\n", i, seqlen); ^ readseq.c:973:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] readseq.c:1075:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d .. ^ readseq.c:1075:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] readseq.c:1087:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); ^ readseq.c:1088:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] else fprintf(foo," %d %d YF\n", seqout, seqlen); ^ readseq.c:1112:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); ^ readseq.c:757:5: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result [-Wunused-result] tmpnam(tempname); ^ readseq.c:911:13: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result [-Wunused-result] freopen( stemp, "w", fout); ^ ureadseq.c: In function ‘seqFileFormatFp’: ureadseq.c:1346:17: warning: format ‘%d’ expects argument of type ‘int *’, but argument 3 has type ‘long int *’ [-Wformat=] sscanf( sp, "%d%d", &nspp, &nlen); ^ ureadseq.c:1346:17: warning: format ‘%d’ expects argument of type ‘int *’, but argument 4 has type ‘long int *’ [-Wformat=] ureadseq.c: In function ‘writeSeq’: ureadseq.c:1595:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] sprintf(numform, "%d", seqlen); ^ ureadseq.c:1624:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); ^ ureadseq.c:1625:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, ^ ureadseq.c:1625:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1639:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seq ^ ureadseq.c:1639:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1649:49: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); ^ ureadseq.c:1659:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ ureadseq.c:1659:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1668:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checks ^ ureadseq.c:1668:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1669:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(outf,"SQ %d BP\n", seqlen); ^ ureadseq.c:1680:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seql ^ ureadseq.c:1680:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1689:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, ^ ureadseq.c:1689:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1695:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ ureadseq.c:1695:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1726:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, ^ ureadseq.c:1748:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, chec ^ ureadseq.c:1748:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1765:22: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, chec ^ ureadseq.c:1765:22: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1771:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", ^ ureadseq.c:1771:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1783:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ ureadseq.c:1783:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1792:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ ureadseq.c:1792:20: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat=] ureadseq.c:1833:38: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] if (numline==1) fprintf(outf,"%-9d ",i+1); ^ /var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccfjE92g.o: In function `main': readseq.c:(.text.startup+0x5ec): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccfjE92g.o: In function `chooseFormat.part.1': readseq.c:(.text+0x36d): warning: the `gets' function is dangerous and should not be used. make: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' make -j1 RNA_wrap.c make: Nothing to be done for 'RNA_wrap.c'. * python2_7: running distutils-r1_run_phase distutils-r1_python_compile /usr/bin/python2.7 setup.py build running build running build_py creating /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA copying ./version_test.py -> /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA copying ./__init__.py -> /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA warning: build_py: byte-compiling is disabled, skipping. running build_ext building '_RNA' extension creating /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7 x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -I../../H -I/usr/include/python2.7 -c RNA_wrap.c -o /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7/RNA_wrap.o -fopenmp RNA_wrap.c: In function ‘my_alifold’: RNA_wrap.c:3803:23: warning: passing argument 1 of ‘alifold’ from incompatible pointer type [-Wincompatible-pointer-types] *energy = alifold(strings, struc); ^ In file included from RNA_wrap.c:3023:0: ../../H/../H/alifold.h:86:8: note: expected ‘const char **’ but argument is of type ‘char **’ float alifold( const char **strings, ^ RNA_wrap.c: In function ‘_wrap_LoopEnergy’: RNA_wrap.c:6691:3: warning: ‘LoopEnergy’ is deprecated [-Wdeprecated-declarations] result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:523:16: note: declared here DEPRECATED(int LoopEnergy(int n1, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_HairpinE’: RNA_wrap.c:6750:3: warning: ‘HairpinE’ is deprecated [-Wdeprecated-declarations] result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:536:16: note: declared here DEPRECATED(int HairpinE(int size, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_initialize_fold’: RNA_wrap.c:6773:3: warning: ‘initialize_fold’ is deprecated [-Wdeprecated-declarations] initialize_fold(arg1); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:547:17: note: declared here DEPRECATED(void initialize_fold(int length)); ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_struct’: RNA_wrap.c:6806:3: warning: ‘energy_of_struct’ is deprecated [-Wdeprecated-declarations] result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:563:18: note: declared here DEPRECATED(float energy_of_struct(const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_struct_pt’: RNA_wrap.c:6860:3: warning: ‘energy_of_struct_pt’ is deprecated [-Wdeprecated-declarations] result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:582:16: note: declared here DEPRECATED(int energy_of_struct_pt( const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_energy_of_circ_struct’: RNA_wrap.c:6895:3: warning: ‘energy_of_circ_struct’ is deprecated [-Wdeprecated-declarations] result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2); ^ In file included from RNA_wrap.c:3005:0: ../../H/../H/fold.h:601:18: note: declared here DEPRECATED(float energy_of_circ_struct( const char *string, ^ ../../H/../H/fold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_initialize_cofold’: RNA_wrap.c:7360:3: warning: ‘initialize_cofold’ is deprecated [-Wdeprecated-declarations] initialize_cofold(arg1); ^ In file included from RNA_wrap.c:3006:0: ../../H/../H/cofold.h:180:17: note: declared here DEPRECATED(void initialize_cofold(int length)); ^ ../../H/../H/cofold.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_init_pf_fold’: RNA_wrap.c:8155:3: warning: ‘init_pf_fold’ is deprecated [-Wdeprecated-declarations] init_pf_fold(arg1); ^ In file included from RNA_wrap.c:3007:0: ../../H/../H/part_func.h:407:17: note: declared here DEPRECATED(void init_pf_fold(int length)); ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_centroid’: RNA_wrap.c:8186:3: warning: ‘centroid’ is deprecated [-Wdeprecated-declarations] result = (char *)centroid(arg1,arg2); ^ In file included from RNA_wrap.c:3007:0: ../../H/../H/part_func.h:413:18: note: declared here DEPRECATED(char *centroid(int length, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_mean_bp_dist’: RNA_wrap.c:8208:3: warning: ‘mean_bp_dist’ is deprecated [-Wdeprecated-declarations] result = (double)mean_bp_dist(arg1); ^ In file included from RNA_wrap.c:3007:0: ../../H/../H/part_func.h:421:19: note: declared here DEPRECATED(double mean_bp_dist(int length)); ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_expLoopEnergy’: RNA_wrap.c:8293:3: warning: ‘expLoopEnergy’ is deprecated [-Wdeprecated-declarations] result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ In file included from RNA_wrap.c:3007:0: ../../H/../H/part_func.h:426:19: note: declared here DEPRECATED(double expLoopEnergy(int u1, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_expHairpinEnergy’: RNA_wrap.c:8352:3: warning: ‘expHairpinEnergy’ is deprecated [-Wdeprecated-declarations] result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); ^ In file included from RNA_wrap.c:3007:0: ../../H/../H/part_func.h:438:19: note: declared here DEPRECATED(double expHairpinEnergy( int u, ^ ../../H/../H/part_func.h:7:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_Make_bp_profile’: RNA_wrap.c:12008:3: warning: ‘Make_bp_profile’ is deprecated [-Wdeprecated-declarations] result = (float *)Make_bp_profile(arg1); ^ In file included from RNA_wrap.c:3016:0: ../../H/../H/profiledist.h:56:19: note: declared here DEPRECATED(float *Make_bp_profile(int length)); ^ ../../H/../H/profiledist.h:5:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_copy_parameters’: RNA_wrap.c:13464:3: warning: ‘copy_parameters’ is deprecated [-Wdeprecated-declarations] result = (paramT *)copy_parameters(); ^ In file included from RNA_wrap.c:3021:0: ../../H/../H/params.h:126:24: note: declared here DEPRECATED(paramT *copy_parameters(void)); ^ ../../H/../H/params.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_set_parameters’: RNA_wrap.c:13486:3: warning: ‘set_parameters’ is deprecated [-Wdeprecated-declarations] result = (paramT *)set_parameters(arg1); ^ In file included from RNA_wrap.c:3021:0: ../../H/../H/params.h:127:24: note: declared here DEPRECATED(paramT *set_parameters(paramT *dest)); ^ ../../H/../H/params.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ RNA_wrap.c: In function ‘_wrap_PS_dot_plot’: RNA_wrap.c:15036:3: warning: ‘PS_dot_plot’ is deprecated [-Wdeprecated-declarations] result = (int)PS_dot_plot(arg1,arg2); ^ In file included from RNA_wrap.c:3011:0: ../../H/../H/PS_dot.h:195:16: note: declared here DEPRECATED(int PS_dot_plot( char *string, ^ ../../H/../H/PS_dot.h:8:26: note: in definition of macro ‘DEPRECATED’ #define DEPRECATED(func) func __attribute__ ((deprecated)) ^ x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7/RNA_wrap.o -L../../lib -L/usr/lib64 -lRNA -lpython2.7 -o /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/_RNA.so -fopenmp -lstdc++ -s x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1 * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 115: Called src_compile * environment, line 5044: Called distutils-r1_src_compile * environment, line 1522: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' * environment, line 604: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 4578: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3308: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3306: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 881: Called distutils-r1_run_phase 'distutils-r1_python_compile' * environment, line 1513: Called distutils-r1_python_compile * environment, line 1388: Called esetup.py 'build' * environment, line 2419: Called die * The specific snippet of code: * "${@}" || die "${die_args[@]}"; * * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.8::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.8::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:vienna-rna-2.1.8:20160818-050917.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Python' * S: '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'